Terminology for the EMSL Electronic Laboratory Notebook
ELN -The Electronic Laboratory Notebook is a replacement for a paper data notebook. You will use it to keep all of your work in this course – preparatory to the lab sessions, within the lab sessions, and afterwards for putting together your reports. Since you will be working in groups in this course, we wanted you to be able to share all of your information in common with other members of your group. The electronic form of this notebook makes that possible where the paper notebook cannot.
The EMSL Electronic Laboratory Notebook is a web-based application that allows sharing distributed information across groups. Several National Laboratories are developing it for use by laboratory research teams, and we are adapting it for use by laboratory students. By means networking to a server, it can keep track of and make your information accessible regardless of your particular location, or that of your group colleagues. By means of HTML and Java it can capture and display data regardless of the type of computer system you are using, provided it is connected to the Internet.
Content Navigation – In order to find items in your notebook, you will need some reference system for locating and selecting the information entered there. There are two navigation methods. One is a search method, but the most common is a table of contents.
Table of Contents - The ELN shows the arrangement of information as a "tree" of items, depicting the organization as a hierarchy. It looks rather like the iconic display of data in a computer directory. You give each element of information a name and description when you enter it in your group's ELN. This name appears with its corresponding icon in this TOC view.
Structural Units define the principal groupings of information in the ELN.
Chapters are the largest informational groupings in the ELN. You should think of these as dividers you insert in the ELN. You give each a name when you insert it, which is then displayed with the chapter icon - a folder – in the TOC.
Pages are the second largest informational grouping. You should think of these as blank sheets that you insert into a chapter in the ELN, into which you will later enter notes. You give each a name when you insert it, which is then displayed with the page icon - a sheet – in the TOC.
Content Units are the data and descriptive information (metadata) that you enter into your ELN.
Note - You add information to a page in the manner of a note. You give each note a name at the time of its creation to identify your data entry, and a description, - metadata which report the conditions during, and/or motivation for, your entry. The name of the note appears along with its icon – a pencil and notepad – in the TOC. The actual information you enter is contained in an attachment, or several, which you append to a note before entering the whole in your ELN.
Attachment - An attachment is the vehicle for the data in the ELN. One can be created using any one of the content creators, which are part of your ELN. Some of these creators let you enter data directly – for example a simple text editor for typing in information. Others allow you to enter data indirectly – for example by controlling a data-acquisition instrument, or attaching a formatted document you've made using Word or Excel.
A content unit then is the combination of a metadata note and one or more data attachments, placed in your group's ELN as one composite entry. While you are composing this unit, you may delete its individual items at any time – for example if you make a blunder. But just like a "legal" laboratory notebook, once a content unit is submitted it cannot be altered or deleted. Your only recourse is to make corrections in a new entry.
Content Creators are ELN tools you use for entering information as attachments in your notes. These tools are small application programs. You launch any one of them by clicking the appropriate button corresponding to the desired tool. These buttons all lie in a "toolbox" - a designated area in your ELN.
This is a basic text editor, and you will use it most – to enter observations, comments, and narrative accounts of what you are doing from moment to moment in the lab. You can do simple indenting using leading spaces or the tab key, but you cannot change fonts, colors, or styles of the text created in this editor. Its chief advantage is that is very fast and easy to use.
This editor emulates your writing on a chalk board, and you can use it for combining text with drawing. Use the tool palette along the bottom to create drawings and add text.
You will use this to move any file – document, spreadsheet, image, etc. – from your local ELNcomputer into the note that you are creating, as an attachment. When you launch this, a file dialog box will appear, showing the contents of your computer's directories. You may use this to navigate through the directory structure, choosing any file from your local disk drive that you would like to include in the note you are creating.
You will use an image capture method to make an image file of any area of your computer screen that you select. If you are using a Mac, you will use the capture feature built right into the Mac OS. If you are using a PC, the procedure is a bit different, but the outcome is the same.
On the Mac, simultaneously press Command+Shift+4. The cursor will immediately turn into a "plus/cross" sign. Point to the upper left corner of where you want to capture, and then click down and drag open the rectangle that forms to define the area to you wish to image. Upon release of the clicker, a snap will sound and the image will appear in a file on your Macintosh Main disk. It will have the name <Picture 1> (or "Picture" with some higher number if a previous image has been left on this disk). Then use the load file tool to add this image to the note you are creating.
On a PC, you will need to launch an ELN image capture application by clicking the corresponding button in the toolbox. As with the Mac, click down and drag the rectangle around the area you wish to capture. There will a beep when you start and again when you finish by releasing the clicker. A new image file will be created and added to the entry queue for the note you are creating.
You will use this if you are the rara avis who can write as fast in html as you can on a typewriter. This editor allows type in text, marked up with HTML format tags, and put the resulting file in the entry queue for the note that you are creating.
Control/Entry Window – Interaction between you and an ELN is mediated by means of this window, which the application ELNapp4.5 pops up when launched during the log-in process. This a Java application window, not a Web Browser window, and contains the notebook's TOC for navigating. At its top is a bar of pull-down menus for standard operations, such as Exit for logging out of your notebook properly. It also contains the following:
Toolbox is the area in the control window holding buttons to launch the content creators.
Entry queue is a table listing the items you are gathering in the process of creating note content. It also lists the type/format for the content of each queued item.
Submit and clear buttons next to this entry queue table are for note submission and item clearing, respectively.
Status box displays the name of any unit you have selected in the TOC and the type of unit it is possible to add to the one selected. Directly adjoining are boxes for entering the names and descriptions of both structural and content units that you are going to add.
There are a number of actions that you can perform on the TOC in the control window, in addition to launching creators, naming and describing units, and submitting/clearing entries from the queue:
Selecting - Select an item in the TOC by clicking on its name. The item's name will appear in the status box. Once a notebook item is selected, you can add an appropriate type of unit to it, or perform other actions on or with it, by selecting actions from the control's pull-down menus.
Collapsing and Expanding - Expand and collapse item listings in the TOC by clicking on the plus ("+" to expand) and minus buttons ("-" to collapse) beside an item's name..
Page Viewing Window – A Browser window displays the contents of your ELN. Open this window simply by double-clicking on the icon of any item - page, note, or attachment - in the TOC. This window is separate from the one you have minimized during the log-in process, and shows a detailed view of the names and descriptions of all notes, as well as their attachments, for that page containing the item you have clicked on. When a page is first displayed, the default perspective is full, in which the metadata - names and descriptions - of all notes appear as well as the data contents, literally rendered if possible or symbolically by icons if not. There are a number of actions that you can perform in the page viewing window, each of which gives you a different perspective on the information there. These are:
A hide/show note button on the far right of each note line suppress/reveal all the metadata and data in the note and its attachments. With all the notes on a page hidden, the (remaining) names and entry times display the minimal perspective of its information.
A close/open attachment icon on the far left of each attachment's starting line suppress/reveal the data content of that attachment. With all attachments closed on a page, the (remaining) metadata - names and descriptions – of the notes display the most compact perspective of its information.
Changes in the perspective of the display can be used to advantage for learning the meaning of the experimental record. For example, the compact perspective might be used to reorient yourself to the work after you have been away from it for some period of time.
Downloading – You can recover the original data documents attached to a note by the button provided at the bottom of its display or its icon. This must be done to view the actual data in the case that the attachment was produced in any format for which a browser viewing plug-in is not available. An Excel spreadsheet is an example. But it might also be done to retrieve from the notebook server to your local computer information that you wish to re-purpose. Example would be to analyze data or to include them in the composition of a report.
One final note on the page viewing process relates to your choice of how to prepare your entries for your group's notebook. You will observe that the Page Viewing Window is actually a Web Browser window. This means that the page itself is an html document created by the ELN server to render your information visible for you to read. Your choice on how to compose your ELN data entries should hinge on whether you need to see your data actually displayed directly in your notebook, or whether you can make do with an indirect, iconic display, waiting to download and actually display information with the application which originally encoded it. Since you will be working in a group and likely be working on a variety of computers in different places to analyze results and produce a report, the availability of the external applications might be something to consider before entering your data in your group's ELN.
Grant screens - This is a "request" for privileges to execute programs and create files on your local computer. (It is electronically signed by the company - Battelle Memorial Institute – as a certified assurance that these programs and their operation is not malicious.) The notebook software will not delete files on your hard drive, but it does need to store and update status files when you make additions to the notebook.
Group username and password - Your group will be given a group username and a group password to be used in common each time any of you wishes to use your group's ELN.
More than one of your group may simultaneously use your common ELN from different computers. However, only one individual may use any ELN on a given computer at the same time.
As a footnote – be prepared to encounter group log-in twice on each occasion you use your ELN. The first occurs upon entry into the ELN, and the second occurs the first time you call to view page content after you have already been operating with the control window. This second is necessitated because your ELN on its server stores its structural and content information in different, separate places with group security on both sites.
Individual Log-in – The second order of security is at an individual level. This secures the authorship of your contributions to your group's notebook by name-stamping each of your entries with your own name.
Individual username and password - The first time you use your group's ELN you will be asked to log in as a new user, and choose your personal password. Thereafter, on subsequent occasions your name will appear in the pull-down menu of the username box where you may select it. The name you use here will appear on every entry you make in the ELN.
Individual email address - The email address you enter here will be used in links (to your email) attached to your name throughout the ELN to facilitate intra-group communication. You should use therefore the email service that you check most often.